Metabolomics Software Tools. Xiuxia Du, Paul Benton, Stephen Barnes

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1 Metabolomics Software Tools Xiuxia Du, Paul Benton, Stephen Barnes

2 Outline 2 Introduction Software Tools for LC-MS metabolomics Software Tools for GC-MS metabolomics Software Tools for Statistical Analysis

3 Introduction LC-MS data analysis workflow GC-MS data analysis workflow data preprocessing feature extraction statistical analysis deconvolution statistical analysis compound identification compound identification pathway analysis pathway analysis 3

4 Software Tools for LC-MS Commercial MassHunter Agilent MetQuest Thermo Scientific MetWorks Thermo Scientific Multiple Mass Defect Filter Thermo Scientific Progenesis QI Waters XCMS plus Sciex and more 4

5 Software Tools for LC-MS Free Insilicos Viewer ProteoWizard SeeMS: interactive viewer for mass spec data files (Windows only) MSConvert: convert between various file formats MZmine 2: LC-MS data processing MetaboSearch: perform mass-based metabolite search simultaneously against four major metabolite databases MetaboAnalyst: a web server for metabolomics data analysis and more 5

6 Data format Proprietary data formats: need vendor library functions to access Open data formats: free library functions to access netcdf mzdata mzxml mzml Company File extension Agilent.D Sciex Theomo Waters.WIFF.RAW.RAW 6

7 InsilicosViewer 7

8 Insilicos Viewer Raw data viewer total ion chromatogram MS and MS/MS 8

9 ProteoWizard 9

10 ProteoWizard: SeeMS A data viewer Can read these open data formats mzml mzxml 10

11 ProteoWizard: SeeMS Raw data viewer total ion chromatogram spectrum list of scans 11

12 ProteoWizard: MSConvert Data format converter 12

13 ProteoWizard: MSConvert Supported data formats Read: open formats, vendor formats Write: open formats Filters and transformation mslevel Peak picking Zero samples ETD filter Threshold peak filter Charge state predictor Activation Subset 13

14 MZmine 2 14

15 MZmine 2 LC-MS metabolomics data processing, analysis, and visualization Supported open data formats NetCDF mzdata mzml mzxml 15

16 Raw data import list of scans in raw files MS scans in blue MS/MS scans in red # sequential retention time MS level type of spectrum p = profile c = centroid t = thresholded polarity of ionization + = positive - = negative? = unknown 16

17 Raw data visualization brings up Right click on the file name 17

18 Raw data visualization double click TIC total ion chromatogram brings up spectrum 18

19 Raw data visualization 2D view 19

20 Raw data visualization rotate to find the best perspective 3D view 20

21 Data pocessing Workflow Raw data import (optional) Raw data methods / Filtering Peak detection Isotopic peak grouping (optional) Identification of fragments, adducts, and peak complexes (optional) Normalization of retention time Alignment (optional) Gap filling (optional) Normalization of peak heights / areas (optional) Identification using database search, formula prediction, etc. Data analysis and export 21

22 Peak detection Mass detection Centroid Exact mass Local maxima Recursive threshold Wavelet transform Chromatogram building Peak deconvolution 22

23 Peak detection Peak detection procedure 23

24 Mass detection Mass detection options click here to bring up the parameter window 24

25 Mass detection Set mass detection parameter 25

26 Mass detection Set mass detection parameter 26

27 Chromatogram building Chromatogram builder 27

28 Chromatogram building Chromatogram builder set parameters 28

29 Chromatogram building After chromatograms are built peak list # ID m/z retention time 29

30 Chromatogram building To display extracted ion chromatograms brings up Right click on the file name 30

31 Chromatogram building Show chromatogram information 31

32 Chromatogram building Show chromatogram information a particular extracted ion chromatogram (EIC) 32

33 Peak deconvolution 33

34 Peak deconvolution Algorithms 34

35 Peak deconvolution Set parameters click here to bring up the parameter window 35

36 Peak deconvolution deconvolution finished 36

37 Peak deconvolution Results 37

38 Alignment Retention time normalization 38

39 Alignment Retention time normalization: set parameters

40 Join aligner Alignment

41 Join aligner: set parameters Alignment

42 Get aligned peak list Alignment

43 Alignment Information on aligned peak list Green: present Red: absent

44 Peak identification Options 44

45 Peak identification By searching custom databases an example custom database 45

46 Peak identification By adduct search: set parameters 46

47 Adduct search results Peak identification 47

48 By online database search Peak identification 48

49 Peak identification Online database search results 49

50 Options and parameters Gap filling 50

51 Gap filling Results and visualization options 51

52 Set visualization parameters Gap filling 52

53 Gap filling Visualization 53

54 Data analysis Options 54

55 Data export Options 55

56 Data export Parameters 56

57 Data export csv format 57

58 MetaboSearch 58

59 MetaboSearch Input data format 59

60 MetaboSearch GUI 60

61 MetaboSearch Steps 61

62 Software tools for GC-MS Metabolomics 62

63 Software Tools for GC-MS Commercial ChromaTOF LECO MassHunter Agilent Free AMDIS: Automated Mass Spectral Deconvolution and Identification System NIST MS Search Tagfinder 63

64 AMDIS Raw data visualization 64

65 AMDIS Result visualization 65

66 NIST MS Search GUI 66

67 Software tools for Statistical Analysis 67

68 Stats and Machine Learning Commercial SIMCA Mass Profiler Professional (MPP) Agilent and more Free MetaboAnalyst R 68

69 MetaboAnalyst 69

70 Other software tools COMSPARI COMparison of SPectral And Retention Information MathDAMP Mathematica package for Differential Analysis of Metabolite Profiles MSFACTs and many more Metabolomics Spectral Formatting, Alignment and Conversion Tools 70

71 Thank You

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